This interview, the 90th in our series, was published in Development last year. 

Hox genes instruct positional identity along the anterior-posterior axis of the animal body. A new paper in Development addresses the question of how similar Hox genes can define diverse cell fates, using mouse motor neurons as a model. To hear more about the work, we caught up with the paper’s two first authors, PhD students Milica Bulajić and Divyanshi Srivastava, and their respective supervisors Esteban Mazzoni (Associate Professor of Biology at New York University, USA) and Shaun Mahony (Assistant Professor of Biochemistry & Molecular Biology at Penn State University, USA).

Esteban and Shaun, what questions are your labs trying to answer, and how did you come to collaborate on this project?

EM: To understand cell differentiation, we focus on investigating how transcription factors control transcription and establish long-lasting epigenetic memories. With this knowledge, we then aim to control cell fate at will for clinical applications.

SM: We develop machine learning applications to understand gene regulatory systems. We particularly focus on understanding how transcription factors find their binding sites and drive regulatory responses in dynamic contexts such as development.

EM & SM: We began collaborating as postdocs more than a decade ago when ChIP was emerging (back when it was ChIP-chip!), and there were few computational tools. Even back then, we collaborated at a distance, with EM in New York and SM in Boston. EM was developing cellular models to understand cell differentiation at scales and purity compatible with the technology, and SM was developing tools to analyse the data, extract meaningful information and generate hypotheses. This cycle has been going strong ever since: the analyses carried out in SM’s lab have proposed hypotheses about transcription factor selectivity that EM’s lab has tested, and the systems and technologies developed in EM’s lab have inspired many of the computational tools developed in SM’s lab.

Milica and Divyanshi – how did you come to work in the Mazzoni and Mahony labs, and what is the main drive behind your research?

MB: I finished my undergraduate studies in Molecular Biology at the University of Belgrade, Serbia, where I am from. I joined the PhD program at the Department of Biology at New York University in 2014. After spending my first year rotating in different labs, I joined the Mazzoni lab because I really liked the research and enjoyed my rotation project, which was Hox related. I knew that I wanted to continue working on Hox genes and felt supported by Esteban in choosing questions to work on.

DS: When I started my PhD at Penn State, I was keen to work on computational regulatory genomics. I am very excited by the potential of novel computational methods to elucidate complex biology. Therefore, the Mahony lab was a great fit, with Shaun’s expertise in computational biology and the Mazzoni lab’s exciting work on the regulatory biology of cellular differentiation!

How has your research been affected by the COVID-19 pandemic?

EM: Like most institutions, we closed down with two days’ notice. The situation really dawned on me when we turned off equipment for the first time since I opened the lab. However, the hiatus made us focus and plan, and execute the most informative experiments now that we are at 50% output. Thus, it has had a positive side effect.

MB: We were out of the lab for about 3 months so there were some experimental delays, but I’m very lucky that I didn’t lose any work, or need a long time to start things up again. I also had plenty of data to analyse and manuscript edits to incorporate so that has been keeping me busy.

SM: As a computational lab, we were fortunate that we could continue making progress when others lost access to their facilities. But it has still been challenging to adapt to remote research; we miss the conversations and spontaneous debugging sessions that drive computational research forward. As with many others, I’ve personally found it difficult to devote enough time to research while also dealing with remote elementary school and adapting my own courses to a remote format.

DS: COVID-19 has been challenging due to the remote nature of all computational work, but I was fortunate that we had continued access to computational resources, as well as a supportive lab environment, which made it easier to work through the more difficult days.

What was known about the relationship between Hox binding and chromatin accessibility prior to your work?

MB, DS, SM, EM: When we planned these experiments, not much was known about their differential ability to bind inaccessible chromatin. Soon after that, in 2016, Robert White’s group described how some Drosophila Hox factors bind to chromatin. And then, around the time we were writing our paper last summer, a few relevant papers came out. The White group published a more extensive evaluation of all Drosophila Hox proteins showing that accessibility has a role in Hox selectivity, and out of all of the central and posterior Hox proteins, Abd-B stood out in having a higher ability to bind inaccessible sites. This was really interesting for two reasons: first, Hox proteins do have different abilities to bind to inaccessible chromatin; second, it primed our work – how do vertebrate posterior Hox genes (Hox9-13), all of which are fly Abd-B orthologues, behave? Coincidentally, Marie Kmita’s group published a preprint showing that Hox13 paralogs are required to open specific sites during limb development. Finally, Denis Duboule’s group showed similar results in genital development. Thus, the field was coming together.

Can you give us the key results of the paper in a paragraph?

MB, DS, SM, EM: We investigated the binding, transcriptional targets, sequence and chromatin preferences of seven different mammalian Hox proteins in a relevant cell type patterned by Hox genes. We discovered that the ability to engage with inaccessible sites is an important factor that drives Hox binding specificity. This ability seems to be driven by the DNA-binding domain and C-terminus. These results show that Hox specificity models should incorporate sequence preference, co-factor interactions and intrinsic abilities to bind inaccessible chromatin. We believe this can be extended to other homeobox genes (and perhaps other paralogous transcription factor groups) as a binding diversification strategy.

Where Hox proteins show high affinity for inaccessible chromatin, do you think they are acting as so-called ‘pioneer’ factors?

MB, DS, SM, EM: Our results and other studies show clearly that some Hox proteins play a role in ‘opening’ some regions of relatively inaccessible chromatin during differentiation. However, in the strict sense, the term ‘pioneer factor’ is reserved for those transcription factors that have been demonstrated to bind to DNA wrapped around nucleosomes, which subsequently evict nucleosomes. Our data is compatible with some posterior Hox proteins acting as pioneers, but it is now a good hypothesis to test.

What explains the different chromatin affinities – even among paralogs – of the various posterior Hox proteins?

MB, DS, SM, EM: We used multiple different approaches to characterize sequence preferences and found no evidence that sequence explains the different chromatin affinities. For example, we found no sequence preference differences between HOXC9 and HOXC10, or HOXC9 and the other HOX9 paralogs. Our results with the chimeras, made by swapping HOXC10 and HOXC13 DNA-binding domains, show that chromatin affinities seem to be controlled by the homeodomain and C-terminus. As shown with the bHLH family, the different homeodomains could engage the DNA-nucleosome complex in slightly different ways.

When doing the research, did you have any particular result or eureka moment that has stuck with you?

MB: I think for me, the most impactful thing was seeing the binding results for HOXC13, and finding that it binds to very inaccessible chromatin. Similarly, when I made the chimeric Hox proteins, seeing that this ability is controlled by the DNA-binding domain and C-terminus.

DS: For me, observing the difference in chromatin accessibility at HOXC9-only sites compared with other differentially bound Hox transcription factor sites was an exciting moment. And of course, the binding results for HOXC13 were striking.

Observing the difference in chromatin accessibility at HOXC9-only sites compared with other differentially bound Hox transcription factor sites was an exciting moment.

And what about the flipside: any moments of frustration or despair?

MB: Waiting for reviews during the publication process can be stressful. There are always ups and downs when writing a paper, but when it’s finally written and then accepted for publication, it’s a great feeling.

DS: It was challenging to design a differential binding strategy for multiple transcription factors. We took a long time to arrive at analyses that were robust and reproducible, and that could overcome biases related to technical and experimental noise.

What next for you two after this paper?

MB: I am writing another manuscript and scheduling my PhD defence for early 2021. I’m also in the process of looking and applying for jobs.

DS: I am working on developing computational approaches that can interpretably model transcription factor binding sites. I also plan to defend in early 2021, and pursue research-related positions after my PhD.

Where will this story take the Mahony and Mazzoni labs?

EM: For us, it has two logical future paths. First, gaining insights into Hox-dependent positional identity allows for the precise control of in vitro differentiated motor neuron positional fate. Second, it opened a new dimension within homeodomain transcription factor diversification. The small sequence preference variation was always hard to reconcile with their diverse functions. Now, we hypothesize that the ability to engage inaccessible sites provides an orthogonal mechanism for homeobox genes to diversify their binding and, thus, gene regulation.

SM: This project has really brought home the importance of pre-existing chromatin environments in determining transcription factor binding specificity during development. In a parallel project, Divyanshi has also developed neural networks that can interpret how sequence and pre-existing chromatin features predict the binding specificity of a transcription factor. So, the use of these types of approaches to understand how chromatin shapes transcription factor binding (and vice versa) will continue to be a big focus in our lab, especially in terms of being applied to understand the dynamic systems studied in Esteban’s lab.

Finally, let’s move outside the lab – what do you like to do in your spare time in New York and Pennsylvania?

MB: Going for long walks and hikes, and sitting in a park with a good book.

EM: I am an avid sailor, taking me beyond the lab, the city and the continent. Last October, I participated in a trans-Atlantic race.

DS: I like to go cycling, with the rolling hills of central Pennsylvania providing some lovely terrain.

SM: We’re very fortunate in central Pennsylvania to have lots of beautiful parks and trails, and that’s where my family and I like to spend our spare time.

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In our fourth SciArt Profile we meet Priyanka Oberoi, an illustrator, artist and photographer whose work often features scientific themes.

Where are you originally from and what do you work on now?

Originally I am from India, and am an illustrator and photographer by profession. After spending five years studying art in the College of Art in New Delhi and National Institute of Design in Paldi I started my career as a staff photographer for the magazine ‘Sports Illustrated’ in New Delhi, India. From there I moved on to freelancing as an illustrator and photographer full time. This gave be creative freedom to explore and time to increase my skill set. Studio pottery and wall murals are some of the few skills that I added to my portfolio. I started making scientific illustrations 4 years ago in Germany and currently continue the same in Brussels with my husband and five month old baby boy.

When did science first come in to your life?

I studied science and math in school about fifteen years ago. Deriving physics equations and finding the square root from a hypotenuse taught me that I was better suited for something else. While being an artist was never a childhood dream, it definitely became so after school, and I feel extremely fortunate to have found my forte in art.

Science came back in my life when a few scientist friends asked for some drawings. What started with scientific illustrations for journal papers went on to posters and merchandise for conferences, journal covers, gifs explaining various scientific concepts, lab wall art and more. The scope of scientific communication has really caught my imagination.

Who are your artistic influences?

The impressionists with their bold and confident brush strokes have always left me in awe, and Monet, Manet, Van Gogh and Surat adorn my home walls. The Indian artist from Goa Mario Miranda is someone I look up to for inspiration for my pen and inks. The pop colours in Andy Warhol’s screen prints gives me confidence to go crazy with my colour palettes.

What do you think of the relationship between science and art?

I am not a scientist, but the process of creating art certainly has an impact on scientific process. With art, one needs to distil an idea into a single, coherent visual representation. For instance, when I work with client to create a cover art or graphical abstract, a lot of thought goes into which elements faithfully represent the finding, not just for the author’s peers but for the broader audience. This certainly helps streamline scientific thinking. In-fact, I would suggest scientists create graphical abstracts of their work or progress, as it would help with understanding the major focus of the work and improving the planning of experiments.

“With art, one needs to distil an idea into a single, coherent visual representation”

How do you make your art? 

Pen and inks are my specialty when it comes to illustrations. While I make most of my scientific illustrations digitally the comfort of the simple pen and paper are undeniable.

Be it a commissioned work of art or an idea that I want to bring to life, I always start with my little sketch book. I start by writing key words of a particular project, and if the client has any specific requirements then I note them down too, but if not I start with my favourite, a blank canvas. Then comes the mood board: this generates the basic feel of the artwork which includes the colour palette, sketch style, canvas shape and many such details. This gives the client an idea of the route I will take for the project. With these approvals I start with the artwork. Rough sketches start to adorn my sketch book. Some concepts take days to formulate while some just click instantly. These steps give me a clear passage into my final work of art.

I work on a variety of techniques. Sometimes if the requirement demands a painterly quality that I cannot achieve via digital platforms I go back to the traditional canvas or paper with high resolution scans. The bottom line is that the process is super intoxicating and so when one project comes to an end I cannot wait to begin the next!

What are you thinking of working on next?

I am currently working on a board game for the Deutsch museum in Munich – acompletely new challenge with its new set of rules.

Also filling up my sketch book pages is a self initiated project called ‘Danio & Rerio’. A weekly comic strip that I recently started on twitter that embarks on the adventures of two zebrafish and their stints with various fun science experiments.

Apart from commissioned works of art I conduct team building and exploratory workshops. One such workshop includes traditional wooden blocks that I got made in India. These wooden blocks are science themed with a twist used for block printing on bags, t-shirts and pretty much any surface. These workshops are open to any lab that want some reclamation time. This inexpensive activity is fun and refreshes all the members of a lab without planning a formal retreat. One set of workshops are going to be offered to an international school in Brussels for their extra curricular spring and possibly summer sessions.

Conference poster: Molecular origins of Life, Munich 2021

Conference poster: Molecular origins of Life, Munich 2020

Conference poster: Engineering Life from origins to organs, Dresden 2019

Scientific conference posters

Lab Wall Art: ‘Bottoms up life forms’. Commissioned by Dr James Saenz, B CUBE – Center for Molecular Bioengineering, Dresden

Danio & Rerio – My weekly comic strip based on two zebrafish and their adventures with various scientific and fun experiments (more of this can be seen on my twitter handle- PriyankaObero16)

Model Organism Illustrations- These are three of my best seller illustrations available on sale as prints on t-shirts, mugs, phone covers and more on Redbubble

Model Organism Illustrations- These are three of my best seller illustrations available on sale as prints on t-shirts, mugs, phone covers and more on Redbubble

Model Organism Illustrations- These are three of my best seller illustrations available on sale as prints on t-shirts, mugs, phone covers and more on Redbubble

Corona Mandala- I made this illustration in April 2020 during the lockdown when I was confined to the space in my home like the rest of the world, I could only see and hear Corona. Like a mandala it started as a small dot and spread to what feels never ending even today.

Assorted pieces – click for captions

Check out Priyanka’s homepage:

https://cargocollective.com/priyankaoberoi

And her official scientific illustration merchandise shop:

https://www.redbubble.com/people/priyankaoberoi/shop

Follow Priyanka on Twitter: @PriyankaObero16

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The joint CiM-IMPRS graduate program of the International Max Planck Research School – Molecular Biomedicine and Muenster’s Cells in Motion Interfaculty Centre offers positions to pursue PhD projects in the areas of biology, chemistry, physics, mathematics or computer science. We are looking for young scientists with a vivid interest in interdisciplinary projects to image cell dynamics from the subcellular to the patient level. PhD projects range from the analysis of basic cellular processes to clinical translation, from the application of novel biophysical approaches and the generation of mathematical models to the development of new imaging-related techniques and compounds.

Research areas:

Cell and Molecular Biology. Developmental and Stem Cell Biology

Vascular Biology. Immunology

Microbiology. Neurobiology

In vivo Imaging. High Resolution Optical Imaging

Biophysics. Chemical Biology

Label Chemistry. Mathematical Modelling

and more.

Applications for the PhD program can be submitted from 10 February to 4 April 2021. Projects start in October 2021 (earlier starts are possible if desired). Applications can only be submitted via our online system.

For online application and further information go to

www.cim-imprs.de.

We offer 16 fully financed PhD positions. More positions financed by work contracts may be offered depending on availability. Excellent scientific and transferable skills trainings, competitive work contracts or tax-free fellowships as well as support with administrative matters, accommodation, and visas are part of the program. There are no tuition fees. The program language is English. We invite applications from highly qualified and motivated students of any nationality from biological sciences, chemistry, mathematics, computer sciences and physics. Be part of CiM-IMPRS, a program run jointly by the University of Muenster and the Max Planck Institute for Molecular Biomedicine.

Contact: cim-imprs@uni-muenster.de

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Dear Fly people,

We, Jose Casal and Peter Lawrence, have an opportunity to hire a suitably qualified research assistant to help us for 6 months starting anytime from March Ist. Unfortunately we do not yet know if the job could be extended further than that, but if there is anyone who knows flies, is skilled with the confocal microscope and would like to join us briefly we can pay them at the going rate from the remnant of our current grant until the money runs out.

We are in the Zoology Department of the University of Cambridge and work on planar cell polarity in Drosophila

http://making-of-a-fly.me/

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As astronomers look up to the sky to analyze the infinite universe, developmental biologists look at life unfolding, revealing itself under the light of the microscope. Stars above us, embryos below, we wonder about the possible worlds hindered from our sight. These reflections took place at “The Marine Biology Laboratory Practical Course in Developmental Biology – Quintay 2020” in Chile, where a total of 18 students from 9 different countries (Argentina, Brazil, Chile, Colombia, Ecuador, India, Mexico, Puerto Rico and Uruguay) met, fascinated with the broad diversity of animals, range of experimental techniques, and the huge quality of faculty available in this course.

Despite the fact that most of us were working with one of a small number of “model organisms”, we had the unusual chance to observe, describe and perform experiments with flatworms, sea urchins, fruit flies, Zebrafish, African frogs, and chicken embryos. It was an intense 2 week-practical and theoretical course at the facilities of the Quintay Marine Research Center (CIMARQ) of the Andres Bello University. This immersive experience right next to the Pacific seashore of Chile, together with a remarkable array of experts in different fields of developmental biology in a friendly environment, encouraged us to explore some of the frontiers and unanswered questions in developmental biology.

The course began with the Drosophila module, coordinated by Profs. Nipam Patel (MBL, USA) and John Ewer (University of Valparaiso, Chile). We were introduced to the basic aspects of invertebrate embryogenesis, genetics, and the powerful impact of the Drosophila model in Developmental Biology. Nipam was a very engaging lecturer, transmitting us the beauty of visualizing embryos under a confocal microscope, and giving us the most useful advice for nice immunostainings: “You just need to Wash! Wash! Wash! …and have faith”. We got stunning expression patterns of Hox genes in Drosophila embryos that will become part of a joint publication with results from previous versions of this course. Next, Nipam introduced us to Evo-Devo, the possibility of exploring evolution through the lens of development, by analyzing the gene regulatory networks that establish the anterior-posterior axis of the crustacean Parhyale hawaiensis in comparison to Drosophila.

In sea urchin module, directed by the Prof. David McClay (Duke University, USA) or Uncle Dave as he would say, we took advantage of the CIMARQ-Quintay red sea urchin facility, learning some of the classical experiments of early embryogenesis and the morphogenetic events occurring during sea urchin gastrulation. Dave provoked us with inspiring discussions about developmental biology, and enchanted us with his passion earned through his many years in this field. His lectures about how sea urchin embryo development has been understood were like hearing a nine year old kid telling you about his favorite Christmas presents.

We continued with Prof. Cecilia Moens (University of Washington, USA), who engaged us with an inspiring talk about the early development of the zebrafish brain, and then guided us through a debate about employing gene editing tools such as CRISPR/Cas9 for dissecting early developmental processes, not only in Zebrafish but in almost all research organisms present in the course. This discussion was insightful since nowadays we have a vast array of tools for manipulating gene expression at our fingertips. We were able to compare the advantages and limitations of each one, highlighting the importance of conducting the proper experimental controls.

In the planarian module, Prof. Alejandro Sanchez-Alvarado (Stowers Institute, USA) challenged us to test the regenerative capacities of planarians. He proposed we perform experiments from different kinds of amputations to even tissue transplants, experiments that we would follow for the rest of the course. But his module projected outside the lecture room and the lab. He took us to the closest beach to CIMARQ to get samples of the living creatures that inhabit the Quintay coast. We were impressed by the rich animal diversity that lived there of a variety of shapes and colors. For some of us, it was the first time that we could see, touch and study marine organisms such as sea stars, snails, anemones and a variety of worms including planarians.

The first week ended with a lecture by Prof. Alfonso Martinez Arias (University of Cambridge, UK) on gastruloids and mouse stem cells. He engaged us in a discussion about the philosophical aspects of developmental biology. “Do you think a machine can be an embryo?” he said, to our astonished faces. These sorts of questions lit a heated debate. We discussed the manipulation of human stem cells and embryos, the possibility to compute embryonic development and the limitations of modeling biological phenomena. A key idea that emerged from the conversation, was that we should start talking about “research organisms” instead of “model organisms” because ultimately a model organism only models itself. The group was surprised and motivated by the questions, and the conversation was inspiring: at the end of the day, nobody was indifferent.

Led by Profs. Sally Moody (The George Washington University, USA), Roberto Mayor (University College of London, UK), and Fernando Faunes (University Andres Bello, Chile) the Xenopus module then came into the picture. After enlightening and fulfilling lectures, the practical activities were free and diverse. We were able to choose from a variety of different experiments to learn about axis development and the dorsal organizer inductive properties in Xenopus. Starting with different practical techniques to manipulate embryos – even using an eyebrow as a tool – we were challenged to graft neural crest cells from a fluorescent donor embryo into a wild-type host embryo. Despite the high handling complexity of this experiment, many of us succeeded and were able to record the neural crest migrating in living embryos. This module ended up with the presentation of our results and a funny awards ceremony.

To conclude the organism modules, Profs. Andrea Streit (King’s College London, UK), Claudio Stern (University College London, UK), and João Botelho (Pontificia Universidad Católica de Chile) guided us through the fascinating world of chick development. In very didactical, histrionic and immersive lectures with Claudio, we studied concepts such as regulative development and cell states during early chick embryo development. Then, Andrea brought our attention to non-coding regulatory regions in DNA and regulation of gene expression in the context of sense organ development. In the laboratory, we did ex ovo culture of primitive streak stage embryos and we injected DiI or DiO in Hensen´s node and could follow cell fates and see a fluorescent notochord the next day. We also did in ovo culture experiments and tried methods such as electroporation, to introduce morpholinos, and adding beads to the embryos to study limb development. Inspired by the organizer transplant experiments in Xenopus we asked to do something similar with chicken embryos. Andrea, who is an expert in node transplantation, quickly taught us this technique and the next day we were able to discuss the inductive capacity of the node according to the region where it had been transplanted.

A week into the course we had the opportunity to attend the “Developmental Biology Symposium-Quintay 2020”. Researchers from different universities of Chile came to Quintay to share their work, integrated with talks of some professors of the course. It was an amazing event to get to know the high quality and engaging science developed in Chile.

During the course, the most important complementary activities were the student talks in the evenings. Here, we had the opportunity to introduce our own research projects to the whole group in a very comfortable and relaxed setting, enjoying drinks and snacks during the presentations. The variety of research organisms was amazing, from Drosophila, Zebrafish, Medaka, C. elegans, passing through Xenopus, Axolotls, and even Cestodes and wild Planarian species. Even the experimental approaches varied from one to another, from molecular biology to very robust bioinformatics. The discussion that came up was very helpful, adding different classical and new approaches that we could use in our projects. On many occasions, it was so interesting that we kept talking about it in our lab nights, where the fun lasted until late and we would finish our experiments and record our results with a confocal microscope, with essential help from Jaime Espina (University Andres Bello).

Although all these activities sound tough and demanding, occasions to give our minds a break and enjoy a relaxed conversation were not missing. Besides the lunch time and student talks, we were able to organize a BBQ with our professors and fellows. Here, we got to know each other better, discuss in a relaxed atmosphere, and why not?, laugh with some jokes and chat about life (our life, not the embryo’s!). Another memorable activity was a visit to a neighboring beach, where together with some faculty we were able to enjoy a nice picnic next to ocean. All of this highlights how engaging this course is, how interaction between students and professors, even outside a purely academic context, lies at its heart.

To close these awesome weeks, the closing ceremony was presided over by Prof. Ángela Nieto (CSIC-UMH, Spain), with a lecture of the most recent findings of her laboratory, including the blended study of gene expression profiles, the physical, and cellular variations controlling normal development, metastasis, and cell proliferation. Afterwards, the professors awarded Ailen Cervino and Nicolas Cumplido with a well-deserved reward, which will enable them to attend the next “Embryology: Concepts & Techniques in Modern Developmental Biology” MBL course. Finally, we had lunch together on the Quintay coast, enjoying such good company and filled with energy, looking ahead for our own goals.

A year has passed since “Quintay 2020” took place, a few months before the Covid-19 pandemic broke out. We didn’t know then how fortunate we were to carry out face-to-face discussions, share the bench with other students and professors, or even enjoy a BBQ with people from all over the world! Even though much effort has been placed in order to continue with courses and meetings online, being able to experience a practical course like this one in real life, we believe, has transcendental effects on its students, both at the personal and professional level. Hopefully, new generations of Developmental Biologists will draw on the “Quintay experience” in the near future.

Students (co-authors) & Talks:

Juan A Sanchez. Growth coordination within tissue in Drosophila.
Felipe Berti Valer. The Irre cell Recognition Module and ovarian development in Drosophila: the role of the Roughest protein.
Marycruz Flores Flores. Characterization of cell recruitment mechanism driven by vestigial in the imaginal wing disc of Drosophila melanogaster.
Alison Julio. Structural aspects and evolutive conservation of Calpain action in early insect embryogenesis.
Pablo Guzman. The Slit/Robo pathway is required in different stages of the development of the Drosophila lobula plate.
Emiliano Molina. Differential requirement of the t6A modification in tRNAs, between undifferentiated and differentiated cells in Drosophila melanogaster.
Emilio Oviedo. Regeneration in Ecuadorian land and freshwater planarians.
Cristian Reyes. Reprimo genes in cancer and development, what do we know so far?
Nicolas Cumplido. From Devo to Evo: Hox genes and the shaping of the zebrafish caudal fin.
Sruthi Purushothaman. Fgf-signaling is compartmentalized within the mesenchyme and controls proliferation during salamander limb development.
Aitana Castro Colabianchi. The role of Notch1 during the early development.
Ailen Cervino. A conserved role of Furry in cell polarization and morphogenesis.
Diana Carolina Castañeda Cortés. Crossover between stress and tyroid hormone axes in stress-induced sex reversal.
Felipe Gajardo. Transposable elements in zebrafish hypoxic response: What the data has to tell us.
Oscar Javier Ortega Recalde. DNA methylation memory: Understanding epigenetic reprogramming in vertebrates.
Tonatiuh Molina. Betaglycan, a multifunctional accessory.
Jimena Montagne. Cell differentiation and tissue reorganization during the larval metamorphosis of cestodes.
Juan Rodriguez. Regulation of embryonic cell fate decision by histone methylation.

(8 votes)

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In the latest episode of Genetics Unzipped we’re taking a look at the life of JBS Haldane, whose work, writing and dominant personality made him one of the most interesting characters of 20th century genetics.

As well as being an insightful scientist, fearless self-experimenter and artful communicator, Haldane’s political leanings also affected his approach to science – even at the expense of the scientific rigour that he usually applied to his endeavours.

Kat Arney speaks with Samanth Subramanian, author of the new biography A Dominant Character: The Radical Science and Restless Politics of J.B.S. Haldane to find out more about Haldane’s life, work and complex legacy.

Genetics Unzipped is the podcast from The Genetics Society. Full transcript, links and references available online at GeneticsUnzipped.com.

Subscribe from Apple podcasts, Spotify, or wherever you get your podcasts.

And head over to GeneticsUnzipped.com to catch up on our extensive back catalogue.

If you enjoy the show, please do rate and review on Apple podcasts and help to spread the word on social media. And you can always send feedback and suggestions for future episodes and guests to podcast@geneticsunzipped.com Follow us on Twitter – @geneticsunzip

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Yesterday we held the fifth webinar in our series, this time chaired three members of the preLights team – Sundar Naganathan, Irepan Salvador-Martinez and Grace Lim – in celebration of the site’s third birthday.

Below you’ll find recordings of the talks and live Q&A sessions.

Michèle Romanos (from Bertrand Benazeraf’s lab at the Centre de Biologie Integrative in Toulouse)

‘Cell-to-cell heterogeneity in Sox2 and Brachyury expression ratios guides progenitor destiny by controlling their motility.’

Michèle’s preprint can be found here:

https://www.biorxiv.org/content/10.1101/2020.11.18.388611v2

Marc Robinson-Rechavi (University of Lausanne & Swiss Institute of Bioinformatics)

‘The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection’

Marc’s preprint, a collaboration with the lab of Eileen Furlong and led by Jialin Liu, can be found here:

https://www.biorxiv.org/content/10.1101/2020.11.02.364505v2

Meng Zhu (from Magdalena Zernicka Goetz’s lab at the University of Cambridge)

‘Mechanism of cell polarisation and first lineage segregation in the human embryo’

Meng’s preprint can be found here:

https://www.biorxiv.org/content/10.1101/2020.09.23.310680v1

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A Research Associate post is available in the Morphological Evolution Research Group led by Emília Santos in the Department of Zoology at the University of Cambridge. The preferred start date is 1^st May 2020. The successful candidate will join a vibrant and inter-disciplinary research environment with an excellent international reputation. They will work as a key member of our research team investigating the genetic and developmental mechanisms underlying organismal diversification.

More specifically, the Postdoctoral Researcher will investigate neural crest cell evolution in cichlid fishes. Neural crest cells are a multipotent embryonic cell population that emerge from the vertebrate dorsal neural tube during early development. They then delaminate and undergo some of the longest migrations of any embryonic cell type to give origin to multiple derivatives such as pigment cells, neurons and glia of the peripheral nervous system, smooth muscle, craniofacial cartilage and bone. Many of the features that distinguish vertebrates from their chordate relatives are derived from the neural crest, making this multipotent embryonic cell population a key innovation central to vertebrate evolution.

The successful candidate will compare neural crest development across different cichlid fish species harbouring variation in neural crest derived traits (e.g. pigmentation patterns and craniofacial skeleton), to determine when and how variation in neural crest developmental mechanisms shapes adult trait morphology in a set of extremely closely related species. The project will involve the use of diverse setof techniques such as in situ hybridisation gene expression assays, live imaging of fluorescent reporter lines, and single cell RNA sequencing.

We are looking for a highly motivated candidate with a strong interest in evolutionary developmental biology, comparative embryology, and genomics. The Department of Zoology has a strong Evolutionary and Developmental Biology group, with researchers working in a variety of different organisms. The Department provides access to state-of-the-art imaging and sequencing facilities. Furthermore, the Research Associate will work in close collaboration with other groups in Cambridge working on cichlid population genomics (Prof. Richard Durbin) and epigenetics (Prof. Eric Miska).

Applications should include a motivation letter, a CV and contact details for at least two referees (more information here https://www.jobs.cam.ac.uk/job/28629/). We are committed to increasing diversity, equity and inclusiveness in STEM and encourage applications from underrepresented groups.

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A postdoctoral research position is available in the laboratory of Dr. Michael Smutny at the Centre for Mechanochemical Cell Biology at Warwick Medical School, UK. The lab is focused on exploring biochemical and biophysical processes driving cell and tissue morphogenesis during early embryonic development. For a brief overview of the research in the lab, please visit https://mechanochemistry.org/Smutny/research/.

The successful candidate will work in a new state-of-the-art Interdisciplinary Biomedical Research Building (IBRB), which is part of a thriving research community at Gibbet Hill Campus including the School of Life Science, Warwick Medical School and the Centre for Mechanochemical Cell Biology.

The focus of the project will be on identifying biophysical and biochemical determinants controlling collective cell migration of embryonic progenitor cells in the zebrafish embryo. The project will investigate molecular and physical mechanisms underlying polarisation and directed cell migration combining a range of in vivo and in vitro approaches. The suitable candidate will use state-of-the-art microscopy, computational image analysis tools, latest techniques in cell/developmental biology (gene/protein perturbations, optogenetics), biophysical methods and have the possibility to establish interdisciplinary collaborations. Full training in new techniques and career development opportunities will be provided.

Highly motivated candidates with a strong background in advanced microscopy, image processing, biophysical approaches and high interest in interdisciplinary and collaborative research are encouraged to apply. Practical experience in working with a model organism (zebrafish, drosophila or similar) is desired, but not essential. Candidates should be able to work independently, have excellent communication and interpersonal skills, and participate in supervision of students.

For more details about the project and how to apply, please visit Warwick jobs (post 103651-0221), or get in touch for enquires and expression of interest directly to michael.smutny@warwick.ac.uk. The application closing date is 8^th March 2021.

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Bioinformatics scientist positions at the postdoctoral level are available in the lab of Dr. Sabine Dietmann at Washington University School of Medicine in St. Louis, Missouri, USA.  Our research program is dedicated the development of multi-omics and machine learning approaches to the data sets generated in stem cell-based model systems for embryonic development and organoids. (https://informatics.wustl.edu/research-lab-sabine-dietmann). The candidate’s independent research will benefit from our lab’s extensive collaborative network in the Department of Developmental Biology and the Division of Nephrology at Washington University in St Louis and at international institutions. Projects are available in the following areas: (1) comparing developmental trajectories across species (2) machine learning models for cell fate decisions and gene regulatory networks (3) epitranscriptomics in single cells (https://profiles.wustl.edu/en/persons/sabine-dietmann).

We are seeking enthusiastic and talented candidates with high proficiency in scientific programming languages, such as R and Python/PERL. A good understanding of machine learning frameworks in Python (Keras/Tensorflow), experience with creating packages in R or some experience with single cell data analysis and genomics would be very beneficial.

Applicants should have a Ph.D. or master’s degree in Biology, Computer Science, Bioinformatics, Physics or related field plus 2 years of demonstrated relevant research experience.

Consistently ranked among the top 10 US medical schools, Washington University School of Medicine offers a highly interactive and stimulating academic environment for scientists in training, a place where you can be an individual and achieve exceptional things. Washington University in St. Louis is an equal opportunity employer and committed to providing a comprehensive and competitive benefits package. Our lab is located in the Central West End of St. Louis, a vibrant neighborhood adjacent to major cultural institutions.

For further information please contact sdietmann@wustl.edu.

To apply for this position please submit a CV, a cover letter describing your research interests and contact information for two references no later than March 14 to sdietmann@wustl.edu.

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